data<-read.table("graph.txt",sep=" ")
dim(data)
data[1,]
pdf("beagle_concord_hist.pdf")
hist(data[,10],xlim=c(0,100),xlab="Concordance percent",ylab ="counts",main="Beagle imputation accuracy")
dev.off()
pdf("beagle_concord_hist.pdf")
hist(data[,14],breaks=seq(0,100,0.1),xlim=c(0,100),xlab="Concordance percent",ylab ="counts",main="Beagle imputation accuracy")
dev.off()
pdf("beagle_concord_hist.pdf")
hist(data[,14],breaks=seq(0,100,0.01),xlim=c(0,100),ylim=c(0,100),xlab="Concordance percent",ylab ="counts",main="Beagle imputation accuracy")
dev.off()
pdf("beagle_concord_hist.pdf")
hist(data[,14],breaks=seq(0,100,0.01),xlim=c(0,100),ylim=c(0,60),xlab="Concordance percent",ylab ="counts",main="Beagle imputation accuracy")
dev.off()
pdf("imputation_concord_hist.pdf")
hist(data[,10],breaks=seq(0,100,0.01),xlim=c(0,100),ylim=c(0,60),xlab="Concordance percent",ylab ="counts",main="Impute imputation accuracy")
dev.off()
pdf("imputation_concord_hist.pdf")
hist(data[,14],breaks=seq(0,100,0.01),xlim=c(0,100),ylim=c(0,50),xlab="Concordance percent",ylab ="counts",main="Beagle imputation accuracy")
hist(data[,10],breaks=seq(0,100,0.01),xlim=c(0,100),ylim=c(0,50),xlab="Concordance percent",ylab ="counts",main="Impute imputation accuracy")
dev.off()
pdf("scatter_plot.pdf")
plot(data[,10],data[,14],xlim=c(0,100),ylim=c(0,100),main="Beagle vs Impute",xlab="Impute Concordance",ylab="Beagle concordance")
dev.off()
pdf("scatter_plot.pdf")
plot(data[,10],data[,14],xlim=c(0,100),ylim=c(0,100),main="Beagle vs Impute",xlab="Impute Concordance",ylab="Beagle concordance",pch="*")
dev.off()
pdf("scatter_plot.pdf")
plot(data[,10],data[,14],xlim=c(0,100),ylim=c(0,100),main="Beagle vs Impute",xlab="Impute Concordance",ylab="Beagle concordance",pch="*")
abline(lm(data[,14]~data[,10]), col="red")
dev.off()
data[1,]
data[1:10,1]
data[1:10,1:5]
pdf("scatter_plot_beagle_maf.pdf")
plot(data[,5],data[,14],xlim=c(0,1),ylim=c(0,100),main="Beagle Imputation accuracy MAF",xlab="MAF",ylab="Concordance",pch="*")
plot(data[,5],data[,10],xlim=c(0,1),ylim=c(0,100),main="Impute Imputation accuracy MAF",xlab="MAF",ylab="Concordance",pch="*")
dev.off()
pdf("scatter_plot_beagle_maf.pdf")
plot(data[,5],data[,10],xlim=c(0,0.5),ylim=c(0,100),main="Impute Imputation accuracy MAF",xlab="MAF",ylab="Concordance",pch="*")
plot(data[,5],data[,10],xlim=c(0,0.5),ylim=c(0,100),main="Impute Imputation accuracy MAF",xlab="MAF",ylab="Concordance",pch="*")
dev.off()
pdf("scatter_plot_beagle_maf.pdf")
plot(data[,5],data[,14],xlim=c(0,0.5),ylim=c(0,100),main="Beagle Imputation accuracy MAF",xlab="MAF",ylab="Concordance",pch="*")
plot(data[,5],data[,10],xlim=c(0,0.5),ylim=c(0,100),main="Impute Imputation accuracy MAF",xlab="MAF",ylab="Concordance",pch="*")
dev.off()
savehistory("Rscript_allele_comapare.R")
